[med-svn] [repeatmasker-recon] 01/02: Use citation properly, cme fix dpkg-control

[Andreas Tille]

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tille pushed a commit to branch master
in repository repeatmasker-recon.

commit d5ac1e790dfbbcd18d1463683ea584717e08d73b
Author: Andreas Tille <tille at debian.org>
Date:   Tue Feb 2 15:47:12 2016 +0100

    Use citation properly, cme fix dpkg-control
---
 debian/changelog         | 10 ++++++++++
 debian/control           | 33 +++++++++++++++++++++------------
 debian/upstream/metadata | 12 ++++++++++++
 3 files changed, 43 insertions(+), 12 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index cbb7c66..856d348 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+repeatmasker-recon (1.08-2) UNRELEASED; urgency=medium
+
+  * Team upload
+  * Drop pointer to reference from long description and replace it by
+    abstract text (formatted via cme fix dpkg-control which did some
+    more adjustments)
+  * Add citation as debian/upstream/metadata
+
+ -- Andreas Tille <tille at debian.org>  Tue, 02 Feb 2016 15:44:53 +0100
+
 repeatmasker-recon (1.08-1) unstable; urgency=low
 
   * Initial release (Closes: # 796487)
diff --git a/debian/control b/debian/control
index 601350f..1a55c90 100644
--- a/debian/control
+++ b/debian/control
@@ -1,22 +1,31 @@
 Source: repeatmasker-recon
-Section: science
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Olivier Sallou <osallou at debian.org>
-Build-Depends: debhelper (>= 9), help2man
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+               help2man
 Standards-Version: 3.9.6
-Homepage: http://www.repeatmasker.org/
-Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/repeatmasker-recon.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/repeatmasker-recon.git
 Vcs-Git: git://anonscm.debian.org/debian-med/repeatmasker-recon.git
-
+Homepage: http://www.repeatmasker.org/
 
 Package: repeatmasker-recon
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, perl
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         ${perl:Depends}
 Description: finds repeat families from biological sequences
- The RECON package implements a de novo algorithm for the
- indentification of repeat families from biological sequences.  For
- details about the algorithm, see:
+ The RECON package implements a de novo algorithm for the indentification
+ of repeat families from biological sequences.
  .
- Bao Z. and Eddy S.R. (2002) Automated de novo Identification of Repeat
- Sequence Families in Sequenced Genomes. Submitted.
+ The program implements an approach for the de novo identification and
+ classification of repeat sequence families that is based on extensions
+ to the usual approach of single linkage clustering of local pairwise
+ alignments between genomic sequences. The extensions use multiple
+ alignment information to define the boundaries of individual copies of
+ the repeats and to distinguish homologous but distinct repeat element
+ families. When tested on the human genome, this approach was able to
+ properly identify and group known transposable elements. The program,
+ should be useful for first-pass automatic classification of repeats in
+ newly sequenced genomes.
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..9ee27ce
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,12 @@
+Reference:
+  Author: Zhirong Bao and Sean R. Eddy
+  Title: Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes
+  Journal: Genome Research
+  Year: 2002
+  Volume: 12
+  Number: 8
+  Pages: 1269-76
+  DOI: 10.1101/gr.88502 
+  PMID: 12176934
+  URL: http://genome.cshlp.org/content/12/8/1269.short
+  eprint: http://genome.cshlp.org/content/12/8/1269.full.pdf+html

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